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- PDB-5h6s: Crystal structure of Hydrazidase S179A mutant complexed with a su... -

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Basic information

Entry
Database: PDB / ID: 5h6s
TitleCrystal structure of Hydrazidase S179A mutant complexed with a substrate
ComponentsAmidase
KeywordsHYDROLASE / amidase
Function / homologyAmidase / Amidase, conserved site / Amidases signature. / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / amidase activity / 4-oxidanylbenzohydrazide / Amidase
Function and homology information
Biological speciesMicrobacterium sp. HM58-2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAkiyama, T. / Ishii, M. / Takuwa, A. / Oinuma, K. / Sasaki, Y. / Takaya, N. / Yajima, S.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Structural basis of the substrate recognition of hydrazidase isolated from Microbacterium sp. strain HM58-2, which catalyzes acylhydrazide compounds as its sole carbon source
Authors: Akiyama, T. / Ishii, M. / Takuwa, A. / Oinuma, K.I. / Sasaki, Y. / Takaya, N. / Yajima, S.
History
DepositionNov 15, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amidase
B: Amidase
C: Amidase
D: Amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,8698
Polymers206,2614
Non-polymers6094
Water13,097727
1
A: Amidase
C: Amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4354
Polymers103,1302
Non-polymers3042
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-14 kcal/mol
Surface area29270 Å2
MethodPISA
2
B: Amidase
D: Amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4354
Polymers103,1302
Non-polymers3042
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-12 kcal/mol
Surface area29090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.042, 126.478, 123.185
Angle α, β, γ (deg.)90.00, 105.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Amidase


Mass: 51565.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microbacterium sp. HM58-2 (bacteria) / Strain: HM58-2 / Gene: MHM582_3487 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A170QJP8
#2: Chemical
ChemComp-HDH / 4-oxidanylbenzohydrazide / 4-hydroxybenzoic acid hydrazide


Mass: 152.151 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H8N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 727 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1M imidazole, 0.17 M LiSO4, 2M (NH4)2SO4

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 196526 / % possible obs: 97.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 29.9
Reflection shellResolution: 1.8→1.82 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 5.2 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H6T

5h6t


Resolution: 1.8→40.6 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.058 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.098 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19158 9889 5 %RANDOM
Rwork0.1721 ---
obs0.17309 186627 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.018 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å2-0.05 Å2
2---0.25 Å20 Å2
3---0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.8→40.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13737 0 44 727 14508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01914075
X-RAY DIFFRACTIONr_bond_other_d0.0060.0213583
X-RAY DIFFRACTIONr_angle_refined_deg1.361.97819152
X-RAY DIFFRACTIONr_angle_other_deg0.973.00131113
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.87851835
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.16923.024625
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.705152244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.57715156
X-RAY DIFFRACTIONr_chiral_restr0.080.22197
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02116229
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023103
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.971.6547331
X-RAY DIFFRACTIONr_mcbond_other0.971.6547330
X-RAY DIFFRACTIONr_mcangle_it1.5272.4759169
X-RAY DIFFRACTIONr_mcangle_other1.5272.4769170
X-RAY DIFFRACTIONr_scbond_it1.6331.9026744
X-RAY DIFFRACTIONr_scbond_other1.6331.9026745
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5942.779984
X-RAY DIFFRACTIONr_long_range_B_refined3.48920.33515247
X-RAY DIFFRACTIONr_long_range_B_other3.48920.33715248
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.793→1.839 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 681 -
Rwork0.212 13123 -
obs--92.63 %

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